Contacts of the helix formed by residues 421 - 432 (chain B) in PDB entry 3BYH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 421 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418B VAL 3.2 14.1 + - - -
419B ARG 3.2 2.4 + - - -
420B ASN* 1.3 77.2 + - - +
422B TRP* 1.3 63.8 + - - +
423B ILE 3.6 1.8 - - - -
424B LEU* 3.6 6.3 + - - -
425B LEU* 3.2 22.9 + - - +
455B ASN* 4.0 10.3 - - - -
456B CYS* 3.6 21.2 - - - -
459B VAL* 3.8 7.0 - - - +
478B ILE* 5.1 0.4 - - - -
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Residues in contact with TRP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B ASP* 6.1 0.2 - - - +
409B SER* 3.8 9.4 + - - -
418B VAL 5.8 0.2 - - - -
420B ASN* 2.9 25.2 + - - +
421B GLY* 1.3 70.6 - - - -
423B ILE* 1.3 66.1 + - + +
425B LEU* 2.9 18.1 + - + +
426B GLU* 3.1 45.6 + - + +
438B TRP* 3.6 39.0 - + + -
441B ALA* 4.0 12.6 - - + -
442B SER 3.2 28.7 - - - -
443B LYS* 3.6 33.0 - - + +
444B PRO* 3.4 29.0 - - + +
455B ASN* 4.2 7.1 - - - +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 4.1 20.9 - - + -
407B ILE* 3.5 17.5 - - + -
409B SER* 3.8 26.0 - - - +
410B TYR 4.6 4.7 - - - +
411B VAL* 3.7 23.6 - - + -
417B ASP* 3.2 37.0 + - + +
418B VAL* 4.9 10.2 - - + +
420B ASN* 4.5 1.0 + - - +
421B GLY 3.6 0.2 - - - -
422B TRP* 1.3 79.0 - - + +
424B LEU* 1.3 63.3 + - + +
426B GLU* 3.0 21.5 + - - +
427B VAL* 3.0 13.9 + - + +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ILE* 5.7 0.9 - - + -
418B VAL* 3.0 38.3 - - + +
421B GLY* 3.6 5.0 + - - +
422B TRP 3.2 0.6 - - - -
423B ILE* 1.3 80.2 - - + +
425B LEU* 1.3 62.3 + - - +
427B VAL* 3.5 8.4 + - + +
428B LEU* 3.1 28.4 + - - +
459B VAL* 3.8 18.6 - - + -
478B ILE* 3.9 27.6 - - + -
486B ILE* 5.7 4.3 - - + -
489B LEU* 3.8 24.2 - - + -
490B LEU* 4.1 25.4 - - + -
493B LEU* 4.2 15.2 - - + +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY 3.2 14.4 + - - +
422B TRP* 2.9 13.2 + - + +
424B LEU* 1.3 75.7 - - - +
426B GLU* 1.3 58.6 + - - +
428B LEU* 3.2 7.3 + - + -
429B ASP* 2.9 25.5 + - - +
436B VAL* 3.3 31.4 - - + +
438B TRP* 3.7 19.5 - - + -
441B ALA* 3.7 29.6 - - + -
455B ASN* 4.1 23.3 - - + +
458B GLN* 4.2 12.3 - - + +
459B VAL* 3.7 25.8 - - + +
462B ILE* 4.6 0.4 - - + -
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Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE* 3.5 19.4 - - + +
408B ASP* 3.3 32.3 + - - +
409B SER* 2.4 34.8 + - - -
422B TRP* 3.1 34.5 + - + +
423B ILE* 3.0 9.0 + - - +
425B LEU* 1.3 74.0 - - - +
427B VAL* 1.3 65.4 + - - +
429B ASP* 3.1 5.2 + - - +
430B LYS* 3.1 28.0 + - + +
438B TRP* 3.8 15.7 - - + -
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B TRP* 3.9 20.4 - - + -
402B ILE* 3.9 34.1 - - + -
405B LEU* 3.9 23.3 - - + -
407B ILE* 4.5 4.7 - - + -
423B ILE* 3.0 21.9 + - + +
424B LEU* 3.9 11.9 - - + +
426B GLU* 1.3 75.0 - - - +
428B LEU* 1.3 57.2 + - - +
430B LYS* 3.3 6.6 + - - +
431B VAL* 3.0 33.7 + - + +
490B LEU* 5.7 0.4 - - + -
493B LEU* 4.1 17.9 - - + -
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B LEU 3.1 22.3 + - - +
425B LEU* 3.4 12.8 - - + +
427B VAL* 1.3 78.9 - - - +
429B ASP* 1.3 56.8 + - - +
431B VAL* 4.6 3.1 - - + +
432B SER* 2.8 34.4 + - - +
435B SER* 3.3 6.4 + - - +
436B VAL* 3.9 7.2 - - + -
459B VAL* 3.9 40.6 - - + +
462B ILE* 4.0 23.1 - - + -
463B GLY* 5.1 2.7 - - - +
466B LEU* 4.2 21.3 - - + -
468B PHE* 5.3 1.6 - - + -
489B LEU* 5.9 2.2 - - + -
493B LEU* 3.5 28.5 - - + -
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Residues in contact with ASP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LEU 2.9 13.6 + - - +
426B GLU* 3.1 8.5 + - - +
428B LEU* 1.3 76.0 - - - +
430B LYS* 1.3 59.7 + - + +
432B SER 4.1 2.2 - - - -
433B PRO* 3.2 27.9 - - - +
434B SER* 3.4 23.2 + - - -
435B SER* 4.2 1.3 - - - -
436B VAL* 3.5 16.7 + - + +
438B TRP* 3.0 38.5 + - + -
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Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 4.0 26.2 + - + +
406B GLY* 3.5 32.0 + - - -
407B ILE* 4.4 7.4 - - + +
426B GLU* 3.1 18.3 + - + +
427B VAL* 3.6 9.2 - - - +
429B ASP* 1.3 79.7 - - + +
431B VAL* 1.3 67.3 + - + +
432B SER 3.5 0.3 + - - -
433B PRO* 3.8 11.3 - - - +
497B HIS* 4.8 8.0 + - + +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TRP* 4.4 8.7 - - + -
405B LEU* 4.9 2.7 - - + -
427B VAL* 3.0 31.2 + - + +
428B LEU* 4.3 3.8 - - + +
430B LYS* 1.3 79.2 - - + +
432B SER* 1.3 57.8 + - - +
433B PRO* 3.7 4.2 - - - +
466B LEU* 6.3 0.4 - - + -
493B LEU* 4.1 11.0 - - + +
496B PHE* 3.3 35.6 - - + -
497B HIS* 3.4 50.1 - - + +
500B GLN* 4.7 6.9 - - - +
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Residues in contact with SER 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B LEU* 2.8 16.0 + - - +
429B ASP 3.6 0.9 - - - +
431B VAL* 1.3 81.5 - - - +
433B PRO* 1.3 69.3 + - - -
435B SER* 2.7 35.1 + - - -
462B ILE* 5.7 0.2 - - - -
466B LEU* 4.0 22.8 - - - +
496B PHE* 4.3 14.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il